In November 2000, as the Florida recount gripped the nation, a newly elected Democratic senator from New York took a break from an upstate victory tour to address the possibility that Al Gore could wind up winning the popular vote but losing the presidential election.

She was unequivocal. “I believe strongly that in a democracy, we should respect the will of the people,” Hillary Clinton said, “and to me that means it’s time to do away with the Electoral College and move to the popular election of our president.”

Sixteen years later, the Electoral College is still standing, and Mrs. Clinton has followed Mr. Gore as the second Democratic presidential candidate in modern history to be defeated by a Republican who earned fewer votes, in his case George W. Bush.

In her concession speech on Wednesday, Mrs. Clinton did not mention the popular vote, an omission that seemed to signal her desire to encourage a smooth and civil transition of power after a divisive election. But her running mate, Senator Tim Kaine of Virginia, highlighted her higher vote total than Donald J. Trump’s in introducing her.

The disparity left a bitter taste in the mouths of many Democrats, whose party won the country’s national popular vote for the third consecutive election but no longer controls any branch of government.

“If we really subscribe to the notion that ‘majority rules,’ then why do we deny the majority their chosen candidate?” asked Jennifer M. Granholm, a former governor of Michigan.

Mr. Trump himself has been critical of the Electoral College in the past. On the eve of the 2012 election, he called it “a disaster for a democracy” in a Twitter post. Now, after months of railing against what he called a “rigged” election, he has become the unlikely beneficiary of an electoral system that enables a candidate to win the race without winning over the most voters.

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A screen displaying the electoral vote count on Tuesday night in Times Square.CreditGeorge Etheredge for The New York Times

None of Mrs. Clinton’s supporters have gone so far as to suggest that the popular vote tally should delegitimize Mr. Trump’s victory, and the popular-vote margin in Tuesday’s election was in fact narrower than the one that separated Mr. Bush and Mr. Gore in 2000.

But the results are already renewing calls for electoral reform. “I personally would like to see the Electoral College eliminated entirely,” said David Boies, the lawyer who represented Mr. Gore in the Florida recount in 2000. “I think it’s a historical anomaly.”

Defenders of the system argue that it reduces the chances of daunting nationwide recounts in close races, a scenario that Gary L. Gregg II, an Electoral College expert at the University of Louisville, said would be a “national nightmare.”

A variety of factors informed the creation of the Electoral College, which apportions a fixed number of votes to each state based on the size of its congressional delegation. The founding fathers sought to ensure that residents in states with smaller populations were not ignored.

In an era that predated mass media and even political parties, the founders were also concerned that average Americans would lack enough information about the candidates to make intelligent choices. So informed “electors” would stand in for them.

Above all, some historians point to the critical role that slavery played in the formation of the system. Southern delegates to the 1787 Constitutional Convention, most prominently James Madison of Virginia, were concerned that their constituents would be outnumbered by Northerners. The Three-Fifths Compromise, however, allowed states to count each slave as three-fifths of a person — enough, at the time, to ensure a Southern majority in presidential races.

On social media Wednesday, some drew connections between that history and what they perceived as an imbalance in the Electoral College that favors Republicans.

“Electoral college will forever tip balance to rural/conservative/“white”/older voters — a concession to slave-holders originally,” the author Joyce Carol Oates wrote on Twitter.

To its critics, the Electoral College is a relic that violates the democratic principle of one person, one vote, and distorts the presidential campaign by encouraging candidates to campaign only in the relatively small number of contested states.

“I think it is intolerable for democracy,” said George C. Edwards III, a political science professor at Texas A&M University and the author of a book on the Electoral College. “I can’t think of any justification for it, and any justification that is offered doesn’t bear scrutiny.”

But calls to change the system, which would require a constitutional amendment, are likely to fall on deaf ears with Republicans in control of both houses of Congress.

And though there was some momentum for reform after Mr. Gore’s defeat, it dissipated after Mr. Bush and Barack Obama won both the popular and electoral votes in 2004, 2008 and 2012.

Some states have discussed a possibility that would not necessarily require amending the Constitution: jettisoning the winner-take-all system, in which a single candidate is awarded all of a state’s electoral votes — regardless of the popular vote — and instead apportioning them to reflect the breakdown of each state’s popular vote. Two states, Maine and Nebraska, already do this.

But even that approach could face challenges, said Laurence H. Tribe, a professor at Harvard Law School.

For reformers, the best hope may lie in the so-called National Popular Vote Interstate Compact, an agreement among states to award all of their respective electoral votes to the candidate who wins the popular vote in a given election.

So far, 10 states and the District of Columbia have joined the agreement. But it will only go into effect when enough states have signed on to guarantee that the winner of the popular vote would win an election.

For now, it seems, any change still remains a far-off notion.

“I am very mad at James Madison,” said former Representative Barney Frank, a Massachusetts Democrat. “But I don’t think there’s anything I can do about it.”

A version of this article appears in print on , on Page P8 of the New York edition with the headline: Many Call the Electoral College Outmoded. So Why Has It Endured?. Order Reprints | Today’s Paper | Subscribe